CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: ENZYMES AND VITAMINS
General Characteristics of Enzymes
→ enzyme – compound, usually a protein, that acts as
a catalyst for a biochemical reaction.
→ enzymes are not consumed in the reactions.
→ most enzymes are globular proteins.
→ enzymes are the most effective catalysts known.
→ few enzymes are now known to be ribonucleic acids
(RNA).
→ enzymes undergo all the reactions of proteins
including denaturation.
→ enzyme activity is dramatically affected by:
alterations in pH and temperature, and other protein
denaturants.
Enzyme Structure
→ simple enzyme – enzyme composed only of protein
(amino acid chains).
→ conjugated enzymes – enzyme that has a
nonprotein part in addition to a protein part.
→ apoenzyme – protein part of a conjugated enzyme.
→ cofactor – nonprotein part of a conjugated enzyme.
→ holoenzyme – biologically active conjugated
enzyme produced from an apoenzyme and a
cofactor.
Cofactors
→ important for the chemically reactive enzymes.
→ coenzyme – small organic molecule that serves as
a cofactor in a conjugated enzyme.
→ coenzymes are synthesized within the human body
using building blocks obtained from other nutrients.
→ many cofactors are permanently bonded, via
covalent bonds, to the amino acid portion of an
enzyme.
Nomenclature and Classification of Enzymes
→ commonly named with reference to their function
such as type of reaction catalyzed and the substrate
present.
→ substrate – reactant in an enzyme-catalyzed
reaction; the substance upon which the enzyme
“acts.”
Three Important Aspects of the Naming Process
1. The suffix -ase identifies it as an enzyme (substance with
the prefix -ase also means that the reaction involved is
hydrolysis); suffix -in is still found in the names of some
digestive enzymes, e.g., trypsin, chymotrypsin, and
pepsin.
2. Type of reaction catalyzed by an enzyme is often used as
a prefix (e.g., oxidase and hydrolase).
3. Identity of substrate is often used in addition to the type
of reaction (e.g., glucose oxidase).
TRANSCRIBED BY: BUCYOT (BSN 1 – Y1 – 37)
Major Classes of Enzymes
1. Oxidoreductase
→ enzyme that catalyzes an oxidation-reduction
reaction.
→ oxidation – losing of electron/s
→ reduction – gaining of electron/s
→ dehydrogenase – removal of hydrogen atoms.
2. Transferase
→ enzyme that catalyzes the transfer of functional
group from one molecule to another.
→ transaminases – catalyzes the transfer of an amino
group from one molecule to another.
→ kinases – catalyzes the transfer of phosphate group
from ATP to give ADP and a phosphorylated product
(a product containing an additional phosphate
group).
3. Hydrolase
→ enzyme that catalyzes a hydrolysis reaction in which
the addition of a water molecule to a bond causes
the bond to break.
4. Lyase
→ enzyme that catalyzes the addition of a group to a
double bond or the removal of a group to form a
double band in a manner that does not involve
hydrolysis or oxidation.
5. Isomerase
→ enzyme that catalyzes the isomerization
(rearrangement of atom) of a substrate in a reaction,
converting it into a molecule isomeric with itself.
6. Ligase
→ enzyme that catalyzes the bonding together of two
molecules into one with participation of ATP and
water.
Class Reaction Catalyzed
Oxidoreductases oxidation-reductions
Transferase functional group transfer reactions
Hydrolases hydrolysis reactions
reactions involving addition or
Lyases
removal of groups form double bonds
Isomerase isomerisation reactions
reactions involving bond formation
Ligases
coupled with ATP hydrolysis
Models of Enzyme Action
Enzyme Active Site
→ active site – relatively small part of an enzyme’s
structure that is actually involved in catalysis.
→ place where substrate binds to enzyme.
→ formed due to folding and bending of the protein.
→ usually a “crevice like” location in the enzyme.
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 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: ENZYMES AND VITAMINS
→ some enzymes have more than one active site.
Enzymes Substrate-Complex
→ intermediate reaction species that is formed when a
substrate binds to the active site of an enzyme.
→ orientation and proximity are favorable and reaction
is fast.
→ needed for the activity of enzyme
Two Models for Substrate Binding to Enzyme
1. Lock-and-Key Model
→ enzyme has a pre-determined shape for the active
site.
→ only substrate of specific shape can bind with active
site.
2. Induced-Fit Model
→ substrate contact with enzyme will change the shape
of the active site.
→ allows small change in space to accommodate
substrate (e.g., how a hand fits into a glove).
Forces that Determine Substrate Binding
→ h-bonding
→ hydrophobic interactions
→ electrostatic interactions
Enzyme Specificity
→ extent to which an enzyme’s activity is restricted to a
specific type of substrates, a specific type of
chemical bond, or a specific type of chemical
reaction.
Major Types of Enzyme Specificity
1. Absolute Specificity
→ an enzyme will catalyze a particular reaction for only
one substrate
→ catalyzes only one reaction.
→ catalase – enzyme with absolute specificity.
→ most restrictive of all specificities (not common).
→ e.g., urease is an enzyme with absolute specificity.
TRANSCRIBED BY: BUCYOT (BSN 1 – Y1 – 37)
2. Group Specificity
→ enzyme will act only on molecules that have a
specific functional group, such as hydroxyl, amino,
or phosphate groups.
→ involves structurally similar compounds that have the
same functional groups.
3. Linkage Specificity
→ enzyme that will act on a particular type of chemical
bond, irrespective of the rest of the molecular
structure.
→ considered most general of enzyme specificities.
4. Stereochemical Specificity
→ enzyme that acts on a particular stereoisomer.
→ can distinguish between stereoisomers.
→ chirality is inherent in an active site (amino acids are
chiral compounds).
Factors that Affect Enzyme Activity
→ enzyme activity – measure of the rate at which an
enzyme converts substrate to products in a
biochemical reaction.
→ includes temperature, pH, substrate concentration,
and enzyme concentration.
Temperature
→ measure of the kinetic energy (energy of motion) of
molecules.
→ higher temperatures – molecules are moving faster
and colliding more frequently.
→ optimum temperature – temperature at which the
rate of enzyme catalyzed reaction is maximum.
→ higher temperature results in higher kinetic energy
which causes an increase in number of reactant
collisions, therefore there is higher activity.
→ increased temperature (high fever) leads to
decreased enzyme activity.
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 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: ENZYMES AND VITAMINS
pH
→ pH changes affect enzyme activity.
→ drastic changes in pH can result in denaturation of
proteins.
→ optimum pH – pH at which enzyme has maximum
activity.
→ most enzymes have optimal activity in the pH range
of 7.0 – 7.5
→ exception is the digestive enzymes pepsin and
trypsin.
→ pepsin: optimum pH = 2.0
→ trypsin: optimum pH = 8.0
Substrate Concentration
→ substrate concentration – at a constant enzyme
concentration, the enzyme activity increases with
increased substrate concentration.
→ substrate saturation – the concentration at which it
reaches its maximum rate and all of the active sites
are full.
→ turnover number – number of substrate molecules
converted to product per second per enzyme
molecule under conditions of optimum temperature
and pH.
TRANSCRIBED BY: BUCYOT (BSN 1 – Y1 – 37)
Enzyme Concentration
→ enzyme concentration – enzymes are not
consumed in the reactions they catalyze.
→ at a constant substrate concentration, enzyme
activity increases with increase in enzyme
concentration.
→ the greater the enzyme concentration, the greater
the reaction rate.
Extremozyme
→ extremophile – microorganism that thrives in
extreme environments, environments in which
humans and most other forms of life could not
survive.
→ extremozyme – microbial enzyme active at
conditions that would inactivate human enzymes as
well as enzymes present in other types of higher
organisms.
Identified Types of Extremozymes
1. Acidophiles
→ optimal growth at pH levels of 3.0 or below.
2. Alkaliphiles
→ optimal growth at pH levels of 9.0 or above.
3. Halophiles
→ high salinity, a salinity that exceeds 0.2 M needed for
growth.
4. Hyperthermophiles
→ a temperature between 80OC and 121OC needed to
thrive.
5. Piezophiles
→ high hydrostatic pressure needed for growth.
6. Xerophiles
→ extremely dry conditions needed for growth.
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 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: ENZYMES AND VITAMINS
7. Cryophiles
→ temperature of 15OC lower needed for growth.
Enzyme Inhibition
→ enzyme inhibitor – substance that slows or stops
the normal catalytic function of an enzyme by binding
to it.
Reverse Competitive Inhibition
→ competitive enzyme inhibitor – resembles an
enzyme substrate in shape and charge distribution
that it can compete with the substrate for occupancy
of the enzyme’s active site.
→ binds reversibly to an enzyme active site and the
inhibitor remains unchanged (no reaction occurs).
→ enzyme inhibitor complex formation is via weak
interactions (hydrogen bonds, etc.).
→ competitive inhibition can be reduced by simply
increasing the concentration of the substrate.
Reversible Noncompetitive Inhibition
→ noncompetitive enzyme inhibition – molecule that
decreases enzyme activity by binding to a site on an
enzyme other than the active site.
→ causes a change in the structure of the enzyme and
prevents enzyme activity.
→ increasing the concentration of substrate does not
completely overcome inhibition.
→ examples are heavy metal ions.
Irreversible Inhibition
→ irreversible enzyme inhibitor – molecules that
inactivates enzymes by forming a strong covalent
bond to an amino acid side-chain group at the
enzyme’s active site.
→ enzyme is permanently inactivated.
→ inhibitor bonds strongly and increasing substrate
concentration does not reverse the inhibition
process.
→ examples are chemical warfare gases.
Regulation of Enzyme Activity
→ cellular processes continually produce large
amounts of an enzyme and plentiful amounts of
products if the processes are not regulated.
→ general mechanisms involved in regulation:
a. proteolytic enzymes and zymogens covalent
modification of enzymes.
b. feedback control Regulation of enzyme activity
by various substances produced within a cell.
c. the enzymes regulated are allosteric enzymes.
Allosteric Enzymes
→ allosteric enzyme – enzyme with two or more
protein chains (quaternary structure) and two kinds
of binding sites (substrate and regulator).
TRANSCRIBED BY: BUCYOT (BSN 1 – Y1 – 37)
→ characteristics of allosteric enzymes are:
a. all have quaternary structure; composed of two
or more protein subunit.
b. two binding sites for substrates and regulators.
c. active and regulatory binding sites are distinct
from each other in both location and shape.
d. binding of molecule at the regulatory site causes
changes in the overall three-dimensional
structure of the enzyme, including structural
changes at the active site.
→ regulators – substances that bind at regulatory site
of allosteric enzymes; has two major types:
a. positive regulator – activators; increases
enzyme activity.
b. negative regulator (noncompetitive
inhibitor) – inhibitors; decreases enzyme
activity.
Feedback Control
→ process in which activation or inhibition of the first
reaction in a reaction sequence is controlled by a
product of the reaction sequence.
→ regulators of a particular allosteric enzyme may be:
→ products of entirely different pathways of reaction
within the cell.
→ compounds produced outside the cell (hormones).
Proteolytic Enzymes and Zymogens
→ proteolytic enzyme – enzyme that catalyzes the
breaking of peptide bonds that maintain the primary
structure of a protein.
→ most digestive and blood-clotting enzymes are
proteolytic enzymes.
→ zymogen (proenzyme) – inactive precursor of a
proteolytic enzyme.
→ proteolytic enzymes are generated in an inactive
form and then converted to their active form.
Covalent Modification of Enzymes
→ covalent modification – process in which enzyme
activity is altered by covalently modifying the
structure of the enzyme through attachment of a
chemical group to or removal of a chemical group
from a particular amino acid within the enzymes
structure.
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 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: ENZYMES AND VITAMINS
→ most common covalent modification: addition and
removal of phosphate group:
→ phosphate group is often derived from an ATP
molecule.
→ addition of the phosphate (phosphorylation)
catalyzed by a Kinase enzyme
→ removal of the phosphate group
(dephosphorylation) catalyzed by a phosphatase
enzyme.
→ phosphate group is added to (or removed from) the
R group of a serine, tyrosine, or threonine amino acid
residue in the enzyme regulated.
Prescription Drugs that Inhibit Enzyme Activity
ACE Inhibitors
→ stands for angiotensin-converting enzyme.
→ angiotensin – octapeptide hormone involved in
blood pressure regulation.
→ present in the body in active form (zymogen).
Sulfa Drugs
→ antibiotic – substance that kill bacteria or inhibits
their growth.
→ many derivatives of sulfanilamide collectively called
sulfa drugs exhibit antibiotic activities.
→ sulfanilamide is structurally similar to PABA (p-
aminobenzoic acid).
→ many bacteria need PABA to produce coenzyme,
folic acid.
→ sulfanilamide is a competitive inhibitor of enzymes
responsible for converting PABA to folic acid in
bacteria.
→ folic acid deficiency retards bacterial growth and that
eventually kills them.
→ sulfa drugs don’t affect humans because we absorb
folic acid from our diet.
Penicillins
→ accidently discovered by Alexander Fleming in 1928.
→ several naturally occurring penicillins and numerous
synthetic derivatives have been produced.
→ all have structures containing a four-membered
beta-lactam ring fused with a five-membered
thiazolidine ring.
→ selectively inhibits transpeptidase by covalent
modification of serine residue.
→ transpeptidase catalyzes the formation of peptide
cross links between polysaccharides strands in
bacterial cell walls.
Cipro
→ the antibiotic ciprofloxacin hydrochloride (cipro for
short).
→ considered the best broad-spectrum antibiotics
because it is effective against skin and bone
TRANSCRIBED BY: BUCYOT (BSN 1 – Y1 – 37)
infections as well as against infections involving the
urinary, gastrointestinal, and respiratory systems.
→ it is the drug of choice for treatment of traveler’s
diarrhea.
→ bacteria are slow to acquire resistance to cipro.
→ biochemical threats associated with terrorism has
thrust cipro into the spotlight because it is effective
against anthrax.
Medical Uses of Enzyme
→ diagnosis of certain disease; enzymes produced in
certain organ/tissues if found in blood may indicate
certain damage to that organ/tissue.
General Characteristics of Vitamins
→ vitamin – organic compound, essential in small
amounts for the proper functioning of the human
body, that must be obtained from dietary sources
because the body cannot synthesize it.
→ needed in micro and milligram quantities.
→ 1 gram of vitamin b is sufficient for 500,000 people.
→ enough vitamin can be obtained from balanced diet.
→ supplemental vitamins may be needed after illness.
→ many enzymes contain vitamins as part of their
structures – conjugated enzymes.
→ two classes – water soluble and fat soluble.
→ synthetic and natural vitamins are same – 13 known
vitamins.
Water-Soluble Vitamins
Vitamin C
→ humans, monkeys, apes and guinea pigs need
dietary vitamins.
→ co-substrate in the formation of structural protein
collagen.
→ involved in metabolism of certain amino acids.
→ 100 mg/day saturates all body tissues – excess
vitamin is excreted.
→ RDA (mg/day):
a. Great Britain: 30
b. United States and Canada: 60
c. Germany: 75
Vitamin B
→ the preferred and alternative names for the b
vitamins
→ thiamin (vitamin b1)
→ riboflavin (vitamin b2)
→ niacin (nicotinic acid, nicotinamide, vitamin b3)
→ vitamin b6 (pyridoxine, pyridoxal, pyridoxamine)
→ folate (folic acid)
→ vitamin b12 (cobalamin)
→ pantothenic acid (vitamin b5)
→ biotin
→ exhibit structural diversity
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 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: ENZYMES AND VITAMINS

→ major function – b vitamins are components of

coenzymes.

Fat-Soluble Vitamins
Vitamin A
→ vision: in the eye vitamin a combine with opsin
protein to form the visual pigment rhodopsin which
further converts light energy into nerve impulses that
are sent to the brain.
→ regulating cell differentiation – process in which
immature cells change to specialized cells with
function.
→ examples: differentiation of bone marrow cells white
blood cells and red blood cells.
→ maintenance of the health of epithelial tissues via
epithelial tissue differentiation.
→ lack of vitamin a cause such surfaces to become
drier and harder than normal.
→ reproduction and growth: in men, vitamin a
participates in sperm development. in women,
normal fetal development during pregnancy requires
vitamin a.

Vitamin D
→ two forms active in the body: vitamin d2 and d3.
→ sunshine vitamin: synthesized by UV light from sun.
→ it controls correct ratio of Ca and P for bone
mineralization (hardening).
→ as a hormone it promotes Ca and P absorption in
intestine.

Vitamin E
→ four forms of vitamin es: a-, b-, g- and d-vitamin e.
→ alpha-tocopherol is the most active biological active
form of vitamin e.
→ peanut oils, green and leafy vegetables and whole
grain products are the sources of vitamin e.
→ primary function: antioxidant – protects against
oxidation of other compounds.

Vitamin K
→ two major forms; k1 and k2
→ k1 found in dark green, leafy vegetables.
→ k2 is synthesized by bacteria that grow in colon.
→ dietary need supply: ~1/2 synthesized by bacteria
and 1/2 obtained from diet.
→ active in the formation of proteins involved in
regulating blood clotting.

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TRANSCRIBED BY: BUCYOT (BSN 1 – Y1 – 37)